﻿<?xml version="1.0" encoding="utf-8" ?>
<AutomationTest>
  <MummerDefaultParams>
    <Command>mumutil.exe /v /o:TestUtils\MumOutput.txt "TestUtils\Small_Size.fasta" "TestUtils\Search_Small_Size.fasta"</Command>
    <ConsoleCommand>mumutil.exe /v "TestUtils\Small_Size.fasta" "TestUtils\Search_Small_Size.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\MumOutput.txt</ActualOutputFile>
    <VerboseResult>MumUtil v2.0 - Maximal Unique Match Utility Copyright (c) Microsoft 2010, 2011,Processed Reference FastA file,Length of first Sequence,Read/Processing time,File size,Suffix tree construction time,Memory consumed by Suffix tree,Total edges created,Memory per edge,Processed Query FastA file,Number of query Sequences,Average length of query Sequences,Compute GetMumsReference() time,WriteMums() time,Total MumUtil Runtime</VerboseResult>
    <ExpectedOutputFile>TestUtils\Small_Size_MumUtil_Output.txt</ExpectedOutputFile>
  </MummerDefaultParams>
  <MummerDefaultParamsWithEColiData>
    <Command>mumutil.exe /o:TestUtils\EColiMumOutput.txt TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta TestUtils\E-Coli_5Mb_ReadsFile_NC_000913.bd_1X_1.fa</Command>
    <ConsoleCommand>mumutil.exe TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta TestUtils\E-Coli_5Mb_ReadsFile_NC_000913.bd_1X_1.fa</ConsoleCommand>
    <ActualOutputFile>TestUtils\EColiMumOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\EColiMumUtilOutput.txt</ExpectedOutputFile>
  </MummerDefaultParamsWithEColiData>
  <MummerWithMaxMatch>
    <Command>mumutil.exe /v /maxmatch /o:TestUtils\MumOutput.txt "TestUtils\Small_Size.fasta" "TestUtils\Search_Small_Size.fasta"</Command>
    <ConsoleCommand>mumutil.exe /v /maxmatch "TestUtils\Small_Size.fasta" "TestUtils\Search_Small_Size.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\MumOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\Small_Size_MumUtil_Output.txt</ExpectedOutputFile>
  </MummerWithMaxMatch>
  <MummerWithAmbiguity>
    <Command>MumUtil.exe /o:TestUtils\MumOutput.txt /n "TestUtils\Ecoli.500.fasta" "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</Command>
    <ConsoleCommand>MumUtil.exe /n "TestUtils\Ecoli.500.fasta" "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\MumOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\MumUtil_NoAmbiguity_EColi500Output.txt</ExpectedOutputFile>
  </MummerWithAmbiguity>
  <MummerWithMumSwitch>
    <Command>MumUtil.exe /v /mum /o:TestUtils\MumOutput.txt /n "TestUtils\Ecoli.500.fasta" "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</Command>
    <ConsoleCommand>MumUtil.exe /v /mum /n "TestUtils\Ecoli.500.fasta" "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\MumOutput.txt</ActualOutputFile>
    <VerboseResult>MumUtil v2.0 - Maximal Unique Match Utility Copyright (c) Microsoft 2010, 2011,Processed Reference FastA file,Length of first Sequence,Read/Processing time,File size,Suffix tree construction time,Memory consumed by Suffix tree,Total edges created,Memory per edge,Processed Query FastA file,Number of query Sequences,Average length of query Sequences,Compute GetMumsMum() time,WriteMums() time,Total MumUtil Runtime</VerboseResult>
    <ExpectedOutputFile>TestUtils\MumUtil_NoAmbiguity_EColi500Output.txt</ExpectedOutputFile>
  </MummerWithMumSwitch>
  <MummerWithLengthAndBothSwitch>
    <Command>MumUtil.exe /o:TestUtils\MumOutput.txt /l:10 /both /c "TestUtils\Ecoli.500.fasta" "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</Command>
    <ConsoleCommand>MumUtil.exe /l:10 /both /c "TestUtils\Ecoli.500.fasta" "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\MumOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\MumUtil__EColi500Output_WithLength_AndBoth.txt</ExpectedOutputFile>
  </MummerWithLengthAndBothSwitch>
  <NucmerUtilDefaultParams>
    <Command>NucmerUtil.exe /v /o:TestUtils\NucmerOutput.txt "TestUtils\Small_Size.fasta" "TestUtils\Search_Small_Size.fasta"</Command>
    <ConsoleCommand>NucmerUtil.exe /v "TestUtils\Small_Size.fasta" "TestUtils\Search_Small_Size.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\NucmerOutput.txt</ActualOutputFile>
    <VerboseResult>Processed Reference FastA file,Read/Processing time,File Size,Processed Query FastA file,Read/Processing time,Compute time,Write() time</VerboseResult>
    <ExpectedOutputFile>TestUtils\Small_Size_NucmerUtil_Output.txt</ExpectedOutputFile>
  </NucmerUtilDefaultParams>
  <NucmerUtilWithEColiData>
    <Command>NucmerUtil.exe -l:30 /o:TestUtils\EColiNucmerOutput.txt TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta TestUtils\E-Coli_5Mb_ReadsFile_NC_000913.bd_1X_1.fa</Command>
    <ConsoleCommand>NucmerUtil.exe -l:30 TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta TestUtils\E-Coli_5Mb_ReadsFile_NC_000913.bd_1X_1.fa</ConsoleCommand>
    <ActualOutputFile>TestUtils\EColiNucmerOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\EColiNucmerUtilOutput.txt</ExpectedOutputFile>
  </NucmerUtilWithEColiData>
  <NucmerUtilLengthAnchorClusterLengthAndDiagonalSwitches>
    <Command>NucmerUtil.exe -l:300 -m -c:100 -d:100 /o:TestUtils\NucmerOutput.txt "TestUtils\Ecoli.500.fasta" "TestUtils\Ecoli.500.fasta"</Command>
    <ConsoleCommand>NucmerUtil.exe -l:300 -m -c:100 -d:100 "TestUtils\Ecoli.500.fasta" "TestUtils\Ecoli.500.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\NucmerOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\EColi_500_NucmerOutput.txt</ExpectedOutputFile>
  </NucmerUtilLengthAnchorClusterLengthAndDiagonalSwitches>
  <NucmerUtilWithManySwitches>
    <Command>NucmerUtil.exe -b:10 -n -r -x /o:TestUtils\NucmerOutput.txt "TestUtils\Ecoli.500.fasta" "TestUtils\Ecoli.500.fasta"</Command>
    <ConsoleCommand>NucmerUtil.exe -b:10 -n -r -x "TestUtils\Ecoli.500.fasta" "TestUtils\Ecoli.500.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\NucmerOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\EColi.500_NucmerOutputWithManySwitches.txt</ExpectedOutputFile>
  </NucmerUtilWithManySwitches>
  <PadenaUtilDefaultParams>
    <Command>PadenaUtil.exe Assemble -v -o:TestUtils\EColiPadenaOutput.txt "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</Command>
    <ConsoleCommand>PadenaUtil.exe Assemble -v "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\EColiPadenaOutput.txt</ActualOutputFile>
    <VerboseResult>Processed read file,Read/Processing time,File Size,k-mer Length,Compute time,Write contigs time,Total runtime</VerboseResult>
    <ExpectedOutputFile>TestUtils\EColi.500_Padena_Assemble_Output.txt</ExpectedOutputFile>
  </PadenaUtilDefaultParams>
  <PadenaUtilWithScaffold>
    <Command>PadenaUtil.exe Scaffold -k:10 -v -o:TestUtils\PadenaOutput.txt "TestUtils\EColi.500_Padena_Assemble_Output.txt" "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</Command>
    <ConsoleCommand>PadenaUtil.exe Scaffold -k:10 -v "TestUtils\EColi.500_Padena_Assemble_Output.txt" "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\PadenaOutput.txt</ActualOutputFile>
    <VerboseResult>Processed contigs file,Read/Processing time,File Size,Processed reads file,Compute time,Write time,Total runtime</VerboseResult>
    <ExpectedOutputFile>TestUtils\EColi.500_Padena_Scaffold_Output.txt</ExpectedOutputFile>
  </PadenaUtilWithScaffold>
  <PadenaUtilAssembleWithScaffold>
    <Command>PadenaUtil.exe assemblewithscaffold -v -o:TestUtils\EColiPadenaScaffoldOutput.txt "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</Command>
    <ConsoleCommand>PadenaUtil.exe assemblewithscaffold -v "TestUtils\Ecoli.500_WithError_1x_Paired.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\EColiPadenaScaffoldOutput.txt</ActualOutputFile>
    <VerboseResult>Processed read file,Read/Processing time,File Size,Compute time,Write time,Total runtime</VerboseResult>
    <ExpectedOutputFile>TestUtils\EColi_500_Padena_AssembleWithScaffold_Output.txt</ExpectedOutputFile>
  </PadenaUtilAssembleWithScaffold>
  <PadenaUtilAssembleOnEColi>
    <Command>PadenaUtil.exe assemble -o:TestUtils\PadenaOutput.txt -k:25 TestUtils\E-Coli_5Mb_ReadsFile_NC_000913.bd_1X_1.fa</Command>
    <ConsoleCommand>PadenaUtil.exe assemble -k:25 TestUtils\E-Coli_5Mb_ReadsFile_NC_000913.bd_1X_1.fa</ConsoleCommand>
    <ActualOutputFile>TestUtils\PadenaOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\EColiPadenaOutputWithAssemble.txt</ExpectedOutputFile>
  </PadenaUtilAssembleOnEColi>
  <RepeatResolutionUtil>
    <Command>RepeatResolutionUtil.exe -o:TestUtils\RepeatOutput.txt TestUtils\EColiNucmerUtilOutput.txt</Command>
    <ConsoleCommand>RepeatResolutionUtil.exe TestUtils\EColiNucmerUtilOutput.txt</ConsoleCommand>
    <ActualOutputFile>TestUtils\RepeatOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\EColi_RepeatResolutionOutput.txt</ExpectedOutputFile>
  </RepeatResolutionUtil>
  <LayoutRefinementUtil>
    <Command>LayoutRefinementUtil.exe -o:TestUtils\LayoutRefinementUtilOutput.txt TestUtils\EColi_RepeatResolutionOutput.txt</Command>
    <ConsoleCommand>LayoutRefinementUtil.exe TestUtils\EColi_RepeatResolutionOutput.txt</ConsoleCommand>
    <ActualOutputFile>TestUtils\LayoutRefinementUtilOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\EColi_LayoutRefinementOutput.txt</ExpectedOutputFile>
  </LayoutRefinementUtil>
  <ConsensusUtil>
    <Command>ConsensusUtil.exe -o:TestUtils\ConsensusUtilOutput.txt TestUtils\EColi_LayoutRefinementOutput.txt</Command>
    <ConsoleCommand>ConsensusUtil.exe TestUtils\EColi_LayoutRefinementOutput.txt</ConsoleCommand>
    <ActualOutputFile>TestUtils\ConsensusUtilOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\EColi_ConsensusOutput.txt</ExpectedOutputFile>
  </ConsensusUtil>
  <ScaffoldUtil>
    <Command>ScaffoldUtil.exe -k:30 -o:TestUtils\ScaffoldUtilOutput.txt TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta</Command>
    <ConsoleCommand>ScaffoldUtil.exe -k:30 TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta</ConsoleCommand>
    <ActualOutputFile>TestUtils\ScaffoldUtilOutput.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\EColi_ScaffoldUtil_Output.txt</ExpectedOutputFile>
  </ScaffoldUtil>
  <ComparativeUtilDefaultParams>
    <Command>ComparativeUtil.exe "TestUtils\ComparativeTestData\DNA-Medium-Ref.fasta" "TestUtils\ComparativeTestData\DNA-Medium-RefReads-WithError_1.fa"  -o:TestUtils\ComparativeTestData\ComparativeActualOutputDefaultParams.txt</Command>
    <ConsoleCommand>ComparativeUtil.exe "TestUtils\ComparativeTestData\DNA-Medium-Ref.fasta" "TestUtils\ComparativeTestData\DNA-Medium-RefReads-WithError_1.fa"  </ConsoleCommand>
    <ActualOutputFile>TestUtils\ComparativeTestData\ComparativeActualOutputDefaultParams.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\ComparativeTestData\ComparativeExpectedOutputDefaultParams.txt</ExpectedOutputFile>
  </ComparativeUtilDefaultParams>
  <ComparativeUtilWithScaffoldEcoli>
    <Command>ComparativeUtil.exe /s /k:25 "TestUtils\NC_000913.bd.fasta" "TestUtils\NC_000913.bd_1X_1.fa"  -o:TestUtils\ComparativeActualOutputEcoliWithScaffold.txt</Command>
    <ConsoleCommand>ComparativeUtil.exe /s /k:25 "TestUtils\NC_000913.bd.fasta" "TestUtils\NC_000913.bd_1X_1.fa"</ConsoleCommand>
    <ActualOutputFile>TestUtils\ComparativeActualOutputEcoliWithScaffold.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\ComparativeExpectedOutputEcoliWithScaffold.txt</ExpectedOutputFile>
  </ComparativeUtilWithScaffoldEcoli>
  <ComparativeUtilEcoliDefaultParams>
    <Command>ComparativeUtil.exe "TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta" "TestUtils\E-Coli_5Mb_ReadsFile_NC_000913.bd_1X_1.fa"  -o:TestUtils\ComparativeActualEcoliOutputDefaultParams.txt</Command>
    <ConsoleCommand>ComparativeUtil.exe "TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta" "TestUtils\E-Coli_5Mb_ReadsFile_NC_000913.bd_1X_1.fa"</ConsoleCommand>
    <ActualOutputFile>TestUtils\ComparativeActualEcoliOutputDefaultParams.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\ComparativeUtilExpectedOutputEcoli.txt</ExpectedOutputFile>
  </ComparativeUtilEcoliDefaultParams>
  <ComparativeUtilVerbose>
    <Command>ComparativeUtil.exe "TestUtils\ComparativeTestData\DNA-Medium-Ref.fasta" "TestUtils\ComparativeTestData\DNA-Medium-RefReads-WithError_1.fa" -v -o:TestUtils\ComparativeTestData\ComparativeActualOutputDefaultParams.txt</Command>
    <ActualOutputFile>TestUtils\ComparativeTestData\ComparativeActualOutputDefaultParams.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\ComparativeTestData\ComparativeExpectedOutputDefaultParams.txt</ExpectedOutputFile>
    <VerboseResult>Processed reference file,Read/Processing time,File Size,Read/Processing time,Assemble time,Write() time</VerboseResult>
  </ComparativeUtilVerbose>
  <ComparativeUtilWithKmerAndMum>
    <Command>ComparativeUtil.exe /k:7 /m:10 "TestUtils\ComparativeTestData\DNA-Medium-Ref.fasta" "TestUtils\ComparativeTestData\DNA-Medium-RefReads-WithError_1.fa" -o:TestUtils\ComparativeTestData\ComparativeActualOutputWithKmerAndMum.txt</Command>
    <ConsoleCommand>ComparativeUtil.exe /k:7 /m:10 "TestUtils\ComparativeTestData\DNA-Medium-Ref.fasta" "TestUtils\ComparativeTestData\DNA-Medium-RefReads-WithError_1.fa"</ConsoleCommand>
    <ActualOutputFile>TestUtils\ComparativeTestData\ComparativeActualOutputWithKmerAndMum.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\ComparativeTestData\ComparativeExpectedOutputWithKmerAndMum.txt</ExpectedOutputFile>
  </ComparativeUtilWithKmerAndMum>
  <ComparativeUtilWithMeanLengthInsert>
    <Command>ComparativeUtil.exe /i:10 "TestUtils\ComparativeTestData\DNA-Medium-Ref.fasta" "TestUtils\ComparativeTestData\DNA-Medium-RefReads-WithError_1.fa" -o:TestUtils\ComparativeTestData\ComparativeActualOutputWithMeanLengthInsert.txt</Command>
    <ConsoleCommand>ComparativeUtil.exe /i:10 "TestUtils\ComparativeTestData\DNA-Medium-Ref.fasta" "TestUtils\ComparativeTestData\DNA-Medium-RefReads-WithError_1.fa"</ConsoleCommand>
    <ActualOutputFile>TestUtils\ComparativeTestData\ComparativeActualOutputWithMeanLengthInsert.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\ComparativeTestData\ComparativeExpectedOutputWithMeanLengthInsert.txt</ExpectedOutputFile>
  </ComparativeUtilWithMeanLengthInsert>
  <LisUtilDefaultParams>
    <Command>LisUtil.exe "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta" -o:TestUtils\LisUtilActualOutputDefaultParams.txt</Command>
    <ConsoleCommand>LisUtil.exe "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\LisUtilActualOutputDefaultParams.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputDefaultParams.txt</ExpectedOutputFile>
  </LisUtilDefaultParams>
  <LisUtilEcoliDefaultParams>
    <Command>LisUtil.exe "TestUtils\E-Coli_5Mb_ReadsFile_NC_000913.bd_1X_1.fa" "TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta" -o:TestUtils\LisUtilActualOutputEcoliDefaultParams.txt</Command>
    <ConsoleCommand>LisUtil.exe "TestUtils\E-Coli_5Mb_ReadsFile_NC_000913.bd_1X_1.fa" "TestUtils\E-Coli_5Mb_RefFile_NC_000913.bd.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\LisUtilActualOutputEcoliDefaultParams.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputEcoli.txt</ExpectedOutputFile>
  </LisUtilEcoliDefaultParams>
  <LisUtilVerbose>
    <Command>LisUtil.exe /v "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta" -o:TestUtils\LisUtilActualOutputDefaultParams.txt</Command>
    <ActualOutputFile>TestUtils\LisUtilActualOutputDefaultParams.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputDefaultParams.txt</ExpectedOutputFile>
    <VerboseResult>Processed Reference FastA file,Length of first Sequence,Read/Processing time,File Size,Processed Query FastA file,Suffix tree construction time,Number of query Sequences,Average length of query Sequences,Compute GetMumsReference() time,WriteMums() time,Total LisUtil Runtime</VerboseResult>
  </LisUtilVerbose>
  <LisUtilWithMaxMatch>
    <Command>LisUtil.exe /MaxMatch "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta" -o:TestUtils\LisUtilActualOutputWithMaxMatch.txt</Command>
    <ConsoleCommand>LisUtil.exe /MaxMatch "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\LisUtilActualOutputWithMaxMatch.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputWithMaxMatch.txt</ExpectedOutputFile>
  </LisUtilWithMaxMatch>
  <LisUtilWithLisOnly>
    <Command>LisUtil.exe /p "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta" -o:TestUtils\LisUtilActualOutputWithLisOnly.txt</Command>
    <ConsoleCommand>LisUtil.exe /p "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\LisUtilActualOutputWithLisOnly.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputWithLisOnly.txt</ExpectedOutputFile>
  </LisUtilWithLisOnly>
  <LisUtilWithReverseOnly>
    <Command>LisUtil.exe /r "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta" -o:TestUtils\LisUtilActualOutputReverseOnly.txt</Command>
    <ConsoleCommand>LisUtil.exe /r "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\LisUtilActualOutputReverseOnly.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputReverseOnly.txt</ExpectedOutputFile>
  </LisUtilWithReverseOnly>
  <LisUtilWithBoth>
    <Command>LisUtil.exe /b "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta" -o:TestUtils\LisUtilActualOutputBoth.txt</Command>
    <ConsoleCommand>LisUtil.exe /b "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\LisUtilActualOutputBoth.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputBoth.txt</ExpectedOutputFile>
  </LisUtilWithBoth>
  <LisUtilWithNoAmbiguity>
    <Command>LisUtil.exe /n "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta" -o:TestUtils\LisUtilActualOutputNoAmbiguity.txt</Command>
    <ConsoleCommand>LisUtil.exe /n "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\LisUtilActualOutputNoAmbiguity.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputNoAmbiguity.txt</ExpectedOutputFile>
  </LisUtilWithNoAmbiguity>
  <LisUtilWithComplementReverseOnly>
    <Command>LisUtil.exe /r /c "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta" -o:TestUtils\LisUtilActualOutputComplementReverseOnly.txt</Command>
    <ConsoleCommand>LisUtil.exe /r /c "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\LisUtilActualOutputComplementReverseOnly.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputComplementReverseOnly.txt</ExpectedOutputFile>
  </LisUtilWithComplementReverseOnly>
  <LisUtilWithComplementBoth>
    <Command>LisUtil.exe /b /c "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta" -o:TestUtils\LisUtilActualOutputComplementBoth.txt</Command>
    <ConsoleCommand>LisUtil.exe /b /c "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\LisUtilActualOutputComplementBoth.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputComplementBoth.txt</ExpectedOutputFile>
  </LisUtilWithComplementBoth>
  <LisUtilWithShowMatchingStr>
    <Command>LisUtil.exe /s "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta" -o:TestUtils\LisUtilActualOutputShowMatchingStr.txt</Command>
    <ConsoleCommand>LisUtil.exe /s "TestUtils\100K-Ecoli-Ref.fasta" "TestUtils\100K-Ecoli-Query.fasta"</ConsoleCommand>
    <ActualOutputFile>TestUtils\LisUtilActualOutputShowMatchingStr.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\LisUtilExpectedOutputShowMatchingStr.txt</ExpectedOutputFile>
  </LisUtilWithShowMatchingStr>
  <SamUtilsWithImportSAMtoBAM>
    <Command>SAMUtils.exe import "TestUtils\SAMBAMTestData\ActualOutputMediumSizeBam.bam" "TestUtils\SAMBAMTestData\MediumSizeSam.Sam"</Command>
    <ConsoleCommand></ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputMediumSizeBam.bam</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputMediumSizedBam.txt</ExpectedOutputFile>
  </SamUtilsWithImportSAMtoBAM>
  <SamUtilsWithImportBAMtoSAM>
    <Command>SAMUtils.exe import "TestUtils\SAMBAMTestData\ActualOutputMediumSizeSam.sam" "TestUtils\SAMBAMTestData\MediumSizeBam.bam"</Command>
    <ConsoleCommand></ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputMediumSizeSam.sam</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputMediumSizedSam.txt</ExpectedOutputFile>
  </SamUtilsWithImportBAMtoSAM>
  <SamUtilsWithSort>
    <Command>SAMUtils.exe sort "TestUtils\SAMBAMTestData\MediumSizeBam.bam" "TestUtils\SAMBAMTestData\ActualOutputSortedBam.bam"</Command>
    <ConsoleCommand></ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputSortedBam.bam</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputSortedBam.bam</ExpectedOutputFile>
  </SamUtilsWithSort>
  <SamUtilsWithSortByReadNames>
    <Command>SAMUtils.exe sort -n "TestUtils\SAMBAMTestData\MediumSizeBam.bam" "TestUtils\SAMBAMTestData\ActualOutputSortedBamByReadNames.bam"</Command>
    <ConsoleCommand></ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputSortedBamByReadNames.bam</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputSortedBamByReadNames.bam</ExpectedOutputFile>
  </SamUtilsWithSortByReadNames>
  <SamUtilsWithIndex>
    <Command>SAMUtils.exe index "TestUtils\SAMBAMTestData\MediumSizeBam.bam" "TestUtils\SAMBAMTestData\ActualOutputBAMIndex.index"</Command>
    <ConsoleCommand></ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputBAMIndex.index</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedBAMIndex.index</ExpectedOutputFile>
  </SamUtilsWithIndex>
  <SamUtilsWithViewDefaultParams>
    <Command>SAMUtils.exe view "TestUtils\SAMBAMTestData\MediumSizeBam.bam" -o:"TestUtils\SAMBAMTestData\ActualOutputViewDefaultParams.txt"</Command>
    <ConsoleCommand>SAMUtils.exe view "TestUtils\SAMBAMTestData\MediumSizeBam.bam"</ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputViewDefaultParams.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputViewDefaultParams.txt</ExpectedOutputFile>
  </SamUtilsWithViewDefaultParams>
  <SamUtilsWithViewHeaderForSAM>
    <Command>SAMUtils.exe view -h "TestUtils\SAMBAMTestData\MediumSizeBam.bam" -o:"TestUtils\SAMBAMTestData\ActualOutputViewWithHeaderForSAM.txt"</Command>
    <ConsoleCommand>SAMUtils.exe view -h "TestUtils\SAMBAMTestData\MediumSizeBam.bam"</ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputViewWithHeaderForSAM.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputViewWithHeaderForSAM.txt</ExpectedOutputFile>
  </SamUtilsWithViewHeaderForSAM>
  <SamUtilsWithViewHex>
    <Command>SAMUtils.exe view -x "TestUtils\SAMBAMTestData\MediumSizeBam.bam" -o:"TestUtils\SAMBAMTestData\ActualOutputViewWithHex.txt"</Command>
    <ConsoleCommand>SAMUtils.exe view -x "TestUtils\SAMBAMTestData\MediumSizeBam.bam"</ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputViewWithHex.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputViewWithHEX.txt</ExpectedOutputFile>
  </SamUtilsWithViewHex>
  <SamUtilsWithViewMinMapQuality>
    <Command>SAMUtils.exe view -q:10 "TestUtils\SAMBAMTestData\MediumSizeBam.bam" -o:"TestUtils\SAMBAMTestData\ActualOutputViewWithMinMapQuality.txt"</Command>
    <ConsoleCommand>SAMUtils.exe view -q:10 "TestUtils\SAMBAMTestData\MediumSizeBam.bam"</ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputViewWithMinMapQuality.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputViewWithMinMapQuality.txt</ExpectedOutputFile>
  </SamUtilsWithViewMinMapQuality>
  <SamUtilsWithViewOutputBAM>
    <Command>SAMUtils.exe view -b "TestUtils\SAMBAMTestData\MediumSizeBam.bam" -o:"TestUtils\SAMBAMTestData\ActualOutputViewWithOutputBam.txt"</Command>
    <ConsoleCommand>SAMUtils.exe view -b "TestUtils\SAMBAMTestData\MediumSizeBam.bam"</ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputViewWithOutputBam.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputViewWithOutputBam.txt</ExpectedOutputFile>
  </SamUtilsWithViewOutputBAM>
  <SamUtilsWithViewSAMFormat>
    <Command>SAMUtils.exe view -S "TestUtils\SAMBAMTestData\MediumSizeSam.sam" -o:"TestUtils\SAMBAMTestData\ActualOutputViewWithSAMFormat.txt"</Command>
    <ConsoleCommand>SAMUtils.exe view -S "TestUtils\SAMBAMTestData\MediumSizeSam.sam"</ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputViewWithSAMFormat.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputViewWithSAMFormat.txt</ExpectedOutputFile>
  </SamUtilsWithViewSAMFormat>
  <SamUtilsWithViewCompressedBAM>
    <Command>SAMUtils.exe view -u "TestUtils\SAMBAMTestData\MediumSizeBam.bam" -o:"TestUtils\SAMBAMTestData\ActualOutputViewWithUncompressedBAM.txt"</Command>
    <ConsoleCommand>SAMUtils.exe view -u "TestUtils\SAMBAMTestData\MediumSizeBam.bam"</ConsoleCommand>
    <ActualOutputFile>TestUtils\SAMBAMTestData\ActualOutputViewWithUncompressedBAM.txt</ActualOutputFile>
    <ExpectedOutputFile>TestUtils\SAMBAMTestData\ExpectedOutputViewWithUncompressedBAM.txt</ExpectedOutputFile>
  </SamUtilsWithViewCompressedBAM>
  <HelpValidation>
    <LisUtilHelpCommand>LisUtil /h</LisUtilHelpCommand>
    <LisUtilExpectedHelp>TestUtils\ExpectedLisUtilHelp.txt</LisUtilExpectedHelp>
    <ComparativeUtilHelpCommand>ComparativeUtil /h</ComparativeUtilHelpCommand>
    <ComparativeUtilExpectedHelp>TestUtils\ExpectedComparativeUtilHelp.txt</ComparativeUtilExpectedHelp>
    <MumUtilHelpCommand>MumUtil /h</MumUtilHelpCommand>
    <MumUtilExpectedHelp>TestUtils\ExpectedMumUtilHelp.txt</MumUtilExpectedHelp>
    <NucmerUtilHelpCommand>NucmerUtil /h</NucmerUtilHelpCommand>
    <NucmerUtilExpectedHelp>TestUtils\ExpectedNucmerUtilHelp.txt</NucmerUtilExpectedHelp>
    <SamUtilsImportHelpCommand>SamUtils Import</SamUtilsImportHelpCommand>
    <SamUtilsImportExpectedHelp>TestUtils\ExpectedSamUtilsImportHelp.txt</SamUtilsImportExpectedHelp>
    <SamUtilsHelpCommand>SamUtils /h</SamUtilsHelpCommand>
    <SamUtilsExpectedHelp>TestUtils\ExpectedSamUtilsHelp.txt</SamUtilsExpectedHelp>
    <SamUtilsViewHelpCommand>SamUtils View</SamUtilsViewHelpCommand>
    <SamUtilsViewExpectedHelp>TestUtils\ExpectedSamUtilsViewHelp.txt</SamUtilsViewExpectedHelp>
    <SamUtilsMergeHelpCommand>SamUtils Merge</SamUtilsMergeHelpCommand>
    <SamUtilsMergeExpectedHelp>TestUtils\ExpectedSamUtilsMergeHelp.txt</SamUtilsMergeExpectedHelp>
    <SamUtilsSortHelpCommand>SamUtils Sort</SamUtilsSortHelpCommand>
    <SamUtilsSortExpectedHelp>TestUtils\ExpectedSamUtilsSortHelp.txt</SamUtilsSortExpectedHelp>
    <SamUtilsIndexHelpCommand>SamUtils Index</SamUtilsIndexHelpCommand>
    <SamUtilsIndexExpectedHelp>TestUtils\ExpectedSamUtilsIndexHelp.txt</SamUtilsIndexExpectedHelp>
    <ScaffoldUtilHelpCommand>ScaffoldUtil /h</ScaffoldUtilHelpCommand>
    <ScaffoldUtilExpectedHelp>TestUtils\ExpectedScaffoldUtilHelp.txt</ScaffoldUtilExpectedHelp>
    <ConsensusUtilHelpCommand>ConsensusUtil /h</ConsensusUtilHelpCommand>
    <ConsensusUtilExpectedHelp>TestUtils\ExpectedConsensusUtilHelp.txt</ConsensusUtilExpectedHelp>
    <LayoutRefinementUtilHelpCommand>LayoutRefinementUtil /h</LayoutRefinementUtilHelpCommand>
    <LayoutRefinementUtilExpectedHelp>TestUtils\ExpectedLayoutRefinementUtilHelp.txt</LayoutRefinementUtilExpectedHelp>
    <RepeatResolutionUtilHelpCommand>RepeatResolutionUtil /h</RepeatResolutionUtilHelpCommand>
    <RepeatResolutionUtilExpectedHelp>TestUtils\ExpectedRepeatResolutionUtilHelp.txt</RepeatResolutionUtilExpectedHelp>
    <PadenaUtilHelpCommand>PadenaUtil /h</PadenaUtilHelpCommand>
    <PadenaUtilExpectedHelp>TestUtils\ExpectedPadenaUtilHelp.txt</PadenaUtilExpectedHelp>
  </HelpValidation>
</AutomationTest>